CreatePredAlphaCost pred_alpha2k alpha11 T0341.t2k.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha04 alpha11 T0341.t04.alpha.rdb 2 alpha alpha_prev sum CreatePredAlphaCost pred_alpha06 alpha11 T0341.t06.alpha.rdb 2 alpha alpha_prev sum SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \ phobic_fit 2 \ sidechain 5 \ n_ca_c 5 bad_peptide 10 \ bystroff 5 \ soft_clashes 30 backbone_clashes 2 \ break 50 \ pred_alpha2k 2 \ pred_alpha04 2 \ pred_alpha06 2 \ constraints 50 \ hbond_geom 5 \ hbond_geom_backbone 10 \ hbond_geom_beta 50 \ hbond_geom_beta_pair 100 \ missing_atoms 1 # Some residue constraints to twist the helices inwardly. Constraint F131.CB L140.CB -10. 7.0 14.0 5 Constraint F131.CB I141.CB -10. 7.0 14.0 5 Constraint F131.CB A142.CB -10. 7.0 14.0 5 bonus Constraint F131.CB V114.CB -10. 7.0 14.0 5 Constraint L140.CB L166.CB -10. 7.0 14.0 5 Constraint I143.CB L166.CB -10. 7.0 14.0 5 bonus # This is the sheet constraint we don't want. Want to make it a Helix instead. # SheetConstraint (T0341)Y148 (T0341)R151 (T0341)L157 (T0341)G154 hbond (T0341)Y149 1 HelixConstraint (T0341)Y148 (T0341)L157 5 # These are the helix constraints from try2-opt2: HelixConstraint (T0341)V25 (T0341)S39 1 HelixConstraint (T0341)T52 (T0341)L63 1 HelixConstraint (T0341)T74 (T0341)Q87 1 HelixConstraint (T0341)R97 (T0341)G104 1 HelixConstraint (T0341)H123 (T0341)D136 1 HelixConstraint (T0341)P159 (T0341)T170 1 HelixConstraint (T0341)K182 (T0341)A192 1 HelixConstraint (T0341)D209 (T0341)N215 1 HelixConstraint (T0341)S246 (T0341)L259 1 # These are the sheet constraints from try2-opt2 (not including the one we want to get # rid of given above): SheetConstraint (T0341)K8 (T0341)D13 (T0341)E198 (T0341)G203 hbond (T0341)A9 10 SheetConstraint (T0341)A9 (T0341)D13 (T0341)M41 (T0341)V45 hbond (T0341)V10 1 SheetConstraint (T0341)R43 (T0341)N47 (T0341)E71 (T0341)S75 hbond (T0341)F44 1 SheetConstraint (T0341)M91 (T0341)D96 (T0341)A112 (T0341)L117 hbond (T0341)L93 1 SheetConstraint (T0341)V113 (T0341)G116 (T0341)P139 (T0341)A142 hbond (T0341)V114 1 SheetConstraint (T0341)L140 (T0341)I143 (T0341)A174 (T0341)V177 hbond (T0341)A142 1 SheetConstraint (T0341)V200 (T0341)D204 (T0341)L219 (T0341)V223 hbond (T0341)M201 1 SheetConstraint (T0341)G220 (T0341)K224 (T0341)Y241 (T0341)E245 hbond (T0341)L222 1